Greedy Selection of Species for Ancestral State Reconstruction on Phylogenies Elimination Is Better than Insertion 英文参考文献.docVIP

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Greedy Selection of Species for Ancestral State Reconstruction on Phylogenies Elimination Is Better than Insertion 英文参考文献.doc

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Greedy Selection of Species for Ancestral State Reconstruction on Phylogenies Elimination Is Better than Insertion 英文参考文献

GreedySelectionofSpeciesforAncestralState ReconstructiononPhylogenies:EliminationIsBetter thanInsertion GuoliangLi1,JianMa2,LouxinZhang3* 1Computational Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore, 2Department of Bioengineering, University of Illinois at Urbana- Champaign,Urbana,Illinois,UnitedStatesofAmerica,3DepartmentofMathematics,NationalUniversityofSingapore,Singapore,Singapore Abstract Accuratereconstructionofancestralcharacterstatesonaphylogenyiscrucialinmanygenomicsstudies.Westudyhowto select species to achieve the best reconstruction of ancestral character states on a phylogeny. We first show that the marginal maximum likelihood has the monotonicity property that more taxa give better reconstruction, but the Fitch methoddoesnothaveitevenonanultrametricphylogeny.Wefurthervalidateagreedyapproachforspeciesselection using simulation. The validation tests indicate that backward greedy selection outperforms forward greedy selection. In addition,byapplyingourselectionstrategy,weobtainasetofthetenmostinformativespeciesforthereconstructionof thegenomicsequenceoftheso-calledboreoeutherianancestorofplacentalmammals.Thisstudyhasbroadrelevancein comparativegenomicsandpaleogenomicssincelimitedresearchresourcesdonotallowresearcherstosequencethelarge numberofdescendantspeciesrequiredtoreconstructanancestralsequence. Citation:LiG,MaJ,ZhangL(2010)GreedySelectionofSpeciesforAncestralStateReconstructiononPhylogenies:EliminationIsBetterthanInsertion.PLoS ONE5(2):e8985.doi:10.1371/journal.pone.0008985 Editor:I.KingJordan,GeorgiaInstituteofTechnology,UnitedStatesofAmerica ReceivedSeptember18,2009;AcceptedJanuary5,2010;PublishedFebruary4,2010 Copyright:?2010Lietal.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermitsunrestricted use,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding: The research was partially supported by the ARF grant R146-000-109-112. The